@sjcrh/proteinpaint-client 2.222.0 → 2.224.0

package/dist/chunk-J5XV35LN.js

@@ -1,468 +0,0 @@
-import {
-  getDefaultScatterSettings
-} from "./chunk-C7KUMZQM.js";
-import {
-  getDefaultViolinSettings
-} from "./chunk-FZYVPRVQ.js";
-import {
-  getDefaultBoxplotSettings
-} from "./chunk-K2ARLT2A.js";
-import {
-  PlotBase,
-  Tabs,
-  defaultUiLabels,
-  fillTermWrapper,
-  filterRxCompInit,
-  getCurrentCohortChartTypes,
-  getDefaultBarSettings,
-  getDefaultFractionBins,
-  getT0T2defaultQ
-} from "./chunk-4ASBDE27.js";
-import {
-  importPlot
-} from "./chunk-OF6FDDKV.js";
-import {
-  Menu
-} from "./chunk-CNFTQSNE.js";
-import {
-  isNumericTw
-} from "./chunk-JHLF2ZC2.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-HBNB5TRH.js";
-
-// plots/summary.ts
-var SummaryPlot = class _SummaryPlot extends PlotBase {
-  constructor(opts, api) {
-    super(opts, api);
-    this.components = {};
-    // expected class-specific props
-    this.chartsByType = {};
-    this.configTermKeys = ["term", "term0", "term2"];
-    this.type = _SummaryPlot.type;
-    this.dom = this.getDom(opts);
-    this.tabsData = this.getTabsData();
-    this.chartToggles = new Tabs({ holder: this.dom.chartToggles, tabs: this.tabsData, noContent: true });
-    this.components = {
-      plots: {}
-    };
-  }
-  static {
-    this.type = "summary";
-  }
-  preApiFreeze(api) {
-    api.getError = () => {
-      return this.error;
-    };
-  }
-  getDom(opts) {
-    const holder = opts.holder;
-    holder.header.style("padding", 0);
-    const paneTitleDiv = holder.header.append("div").style("display", "inline-block").style("color", "#555").style("padding-left", "7px");
-    return {
-      tip: new Menu({ padding: "0px" }),
-      holder,
-      body: holder.body.style("white-space", "nowrap").style("overflow-x", "auto"),
-      // will hold no data notice or the page title in multichart views
-      errdiv: holder.body.append("div").attr("class", "sja_errorbar").style("display", "none").style("padding", "5px"),
-      loading: holder.body.append("div").style("display", "none").style("padding", "5px").html("Loading ..."),
-      // dom.viz will hold the rendered view
-      viz: holder.body.append("div"),
-      plotDivs: {},
-      paneTitleDiv,
-      paneTitleText: paneTitleDiv.append("div").classed("sjpp-term-header", true).style("display", "inline-block").style("vertical-align", "sub"),
-      chartToggles: paneTitleDiv.append("div").style("display", "inline-block").style("margin-left", "10px"),
-      localRecoverDiv: paneTitleDiv.append("div").style("display", "inline-block"),
-      filterDiv: holder.header.append("div").style("display", "inline-block").style("zoom", 0.9)
-    };
-  }
-  getTabsData() {
-    const callback = (event, tab) => this.tabClickCallback(event, tab);
-    return [
-      {
-        childType: "barchart",
-        label: "Barchart",
-        isVisible: () => true,
-        disabled: () => false,
-        getConfig: async () => {
-          if (!this.config) return;
-          const config = { id: this.id, childType: "barchart" };
-          const { term, term2 } = this.config || {};
-          if (term) {
-            const mode = isNumericTw(term) ? "discrete" : term?.q.mode || "discrete";
-            config.term = await this.getWrappedTermCopy(term, mode);
-          }
-          if (term2) {
-            const mode = isNumericTw(term2) ? "discrete" : term2.q.mode || "discrete";
-            config.term2 = await this.getWrappedTermCopy(term2, mode);
-          }
-          return config;
-        },
-        active: true,
-        callback
-      },
-      {
-        childType: "violin",
-        label: "Violin",
-        disabled: () => false,
-        isVisible: () => isNumericTw(this.config?.term) || isNumericTw(this.config?.term2),
-        getConfig: async () => {
-          const term = this.config?.term;
-          const term2 = this.config.term2;
-          let _term, _term2;
-          this.violinContTerm = isNumericTw(term) ? "term" : "term2";
-          if (this.violinContTerm && this.violinContTerm === "term" || term.q?.mode == "continuous") {
-            _term = await this.getWrappedTermCopy(term, "continuous");
-            _term2 = await this.getWrappedTermCopy(term2, "discrete");
-            this.violinContTerm = "term";
-          } else if (this.violinContTerm && this.violinContTerm === "term2" || term2?.q?.mode == "continuous") {
-            _term = await this.getWrappedTermCopy(term, "discrete");
-            _term2 = await this.getWrappedTermCopy(term2, "continuous");
-            this.violinContTerm = "term2";
-          } else if (term2?.q?.mode == "discrete") {
-            _term = await this.getWrappedTermCopy(term, "discrete");
-            _term2 = await this.getWrappedTermCopy(term2, "continuous");
-            this.violinContTerm = "term2";
-          } else {
-            _term = await this.getWrappedTermCopy(term, "continuous");
-            _term2 = await this.getWrappedTermCopy(term2, "discrete");
-            this.violinContTerm = "term";
-          }
-          const config = { childType: "violin", term: _term, term2: _term2 };
-          return config;
-        },
-        active: false,
-        callback
-      },
-      {
-        childType: "boxplot",
-        label: "Boxplot",
-        disabled: () => false,
-        isVisible: () => isNumericTw(this.config?.term) || isNumericTw(this.config?.term2),
-        getConfig: async () => {
-          const _term = this.config?.term;
-          const _term2 = this.config.term2;
-          let termMode = "continuous", term2Mode = "discrete";
-          this.boxContTerm = isNumericTw(_term) ? "term" : "term2";
-          if (this.boxContTerm && this.boxContTerm === "term" || _term.q?.mode == "continuous") {
-            termMode = "continuous";
-            term2Mode = "discrete";
-            this.boxContTerm = "term";
-          } else if (this.boxContTerm && this.boxContTerm === "term2" || _term2?.q?.mode == "continuous") {
-            termMode = "discrete";
-            term2Mode = "continuous";
-            this.boxContTerm = "term2";
-          } else if (_term2?.q?.mode == "discrete") {
-            termMode = "discrete";
-            term2Mode = "continuous";
-            this.boxContTerm = "term2";
-          }
-          const term = await this.getWrappedTermCopy(_term, termMode);
-          const term2 = await this.getWrappedTermCopy(_term2, term2Mode);
-          const config = {
-            childType: "boxplot",
-            term,
-            term2
-          };
-          return config;
-        },
-        active: false,
-        callback
-      },
-      {
-        childType: "sampleScatter",
-        label: "Scatter",
-        disabled: () => false,
-        isVisible: () => isScatterToggleVisible(this.app.getState(), this.config?.term, this.config?.term2),
-        getConfig: async () => {
-          const _term = await this.getWrappedTermCopy(this.config?.term, "continuous");
-          const _term2 = await this.getWrappedTermCopy(this.config?.term2, "continuous");
-          const config = {
-            childType: "sampleScatter",
-            term: _term,
-            term2: _term2,
-            groups: [],
-            term0: this.config.term0
-          };
-          return config;
-        },
-        active: false,
-        callback
-      }
-    ];
-  }
-  async init(appState) {
-    const state = this.getState(appState);
-    const config = structuredClone(state.config);
-    this.initUi(this.opts, config);
-    if (config?.hidePlotFilter) return;
-    this.components.filter = await filterRxCompInit({
-      app: this.app,
-      vocabApi: this.app.vocabApi,
-      parentId: this.id,
-      holder: this.dom.filterDiv,
-      hideLabel: true,
-      emptyLabel: "+Add new filter",
-      callback: (filter) => {
-        this.app.dispatch({
-          id: this.id,
-          type: "plot_edit",
-          config: { filter }
-        });
-      }
-    });
-  }
-  reactsTo(action) {
-    if (action.type.startsWith("plot_")) {
-      if (action.type.startsWith("plot_")) {
-        return action.id === this.id || action.id == this.parentId;
-      }
-    }
-    if (action.type.startsWith("filter")) return true;
-    if (action.type.startsWith("cohort")) return true;
-    if (action.type == "app_refresh") return true;
-    return false;
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) {
-      throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
-    }
-    return {
-      termfilter: appState.termfilter,
-      config,
-      // quick fix to skip history tracking as needed
-      _scope_: appState._scope_
-    };
-  }
-  async main() {
-    delete this.error;
-    this.dom.errdiv.style("display", "none").html("");
-    this.dom.loading.style("display", "");
-    this.config = await this.getMutableConfig();
-    this.maySetSandboxHeader();
-    if (!this.components.plots[this.config.childType]) {
-      await this.setComponent(this.config);
-    }
-    this.dom.loading.style("display", "none");
-    this.render();
-    const activeTabIndex = this.tabsData.findIndex((tab) => tab.childType == this.config.childType);
-    this.chartToggles.update(activeTabIndex);
-    const numVisTabs = this.tabsData.filter((d) => d.isVisible()).length;
-    if (numVisTabs > 1) this.dom.chartToggles.style("display", "inline-block");
-    else this.dom.chartToggles.style("display", "none");
-  }
-  maySetSandboxHeader() {
-    const { term, term2, headerText, assayCohortTitle } = this.config;
-    const mainTerm = term.getTitleText?.() || term.term.name;
-    const _headerPretext = headerText ? `${headerText} ` : "";
-    const _headerSuffix = assayCohortTitle ? ` (${assayCohortTitle})` : "";
-    const titleBase = mainTerm + _headerSuffix;
-    if (term2?.type) {
-      this.dom.paneTitleText.text(`${_headerPretext}${term2.getTitleText?.() || term2.term.name} vs ${titleBase}`);
-    } else {
-      this.dom.paneTitleText.text(`${_headerPretext}${titleBase}`);
-    }
-  }
-  async setComponent(config) {
-    const _ = await importPlot(config.childType, `unsupported childType='${config.childType}'`);
-    this.dom.plotDivs[config.childType] = this.dom.viz.append("div");
-    const componentOpts = {
-      app: this.app,
-      holder: this.dom.plotDivs[config.childType],
-      id: this.id,
-      parent: this.api
-    };
-    if (config.parentId) componentOpts.parentId = config.parentId;
-    this.components.plots[config.childType] = await _.componentInit(componentOpts);
-  }
-  destroy() {
-    this.dom.holder.app_div.selectAll("*").remove();
-    this.dom.holder.app_div.remove();
-    for (const key in this.dom) {
-      delete this.dom[key];
-    }
-  }
-  initUi(opts, config) {
-    this.dom.paneTitleText.text(config.term.term.name);
-    this.chartToggles.main();
-  }
-  async tabClickCallback(event, tab) {
-    if (!tab || !tab.getConfig) return;
-    let config;
-    try {
-      this.dom.viz.style("display", "none");
-      this.dom.loading.style("display", "");
-      config = await tab.getConfig();
-      this.dom.loading.style("display", "none");
-      this.dom.viz.style("display", "");
-      if (config)
-        this.app.dispatch({
-          type: "plot_edit",
-          id: this.id,
-          config
-        });
-    } catch (e) {
-      this.dom.loading.style("display", "none");
-      this.error = e;
-      this.dom.errdiv.style("display", "").html(`Error: ${e.message || e.error || e}`);
-    }
-  }
-  async getWrappedTermCopy(term, mode) {
-    if (!term) return;
-    const tw = structuredClone(term);
-    tw.q.mode = mode;
-    if (tw.type === "TermCollectionTWFraction") {
-      if (mode === "discrete" && tw.q.type !== "regular-bin" && tw.q.type !== "custom-bin") {
-        tw.q = {
-          mode: "discrete",
-          type: "custom-bin",
-          lst: getDefaultFractionBins(),
-          denominators: tw.q.denominators,
-          numerators: tw.q.numerators
-        };
-      } else if (mode === "continuous") {
-        tw.q = {
-          mode: "continuous",
-          denominators: tw.q.denominators,
-          numerators: tw.q.numerators
-        };
-      }
-    }
-    await fillTermWrapper(tw, this.app.vocabApi);
-    return tw;
-  }
-  render() {
-    for (const childType of Object.keys(this.components.plots)) {
-      const chart = this.components.plots[childType];
-      if (chart.type != this.config.childType) {
-        this.dom.plotDivs[chart.type].style("display", "none");
-      }
-    }
-    this.dom.plotDivs[this.config.childType].style("display", "");
-  }
-  getChartImages() {
-    const chart = this.components.plots[this.config.childType];
-    if (chart?.getChartImages) {
-      return chart.getChartImages();
-    }
-    return null;
-  }
-};
-var summaryInit = getCompInit(SummaryPlot);
-var componentInit = summaryInit;
-async function getPlotConfig(opts, app) {
-  try {
-    await app.opts?.getPlotConfig_mutateSummary?.(opts);
-    if (!opts.term) throw new Error("summary getPlotConfig: opts.term{} missing");
-    opts.term = await fillTermWrapper(
-      opts.term,
-      app.vocabApi,
-      opts.term.q || { geneVariant: { type: "predefined-groupset" } }
-    );
-    if (opts.term2)
-      opts.term2 = await fillTermWrapper(
-        opts.term2,
-        app.vocabApi,
-        opts.term2.bins || opts.term2.q ? void 0 : getT0T2defaultQ()
-      );
-    if (opts.term0)
-      opts.term0 = await fillTermWrapper(
-        opts.term0,
-        app.vocabApi,
-        opts.term0.bins || opts.term0.q ? void 0 : getT0T2defaultQ()
-      );
-    if (opts.colorTW) opts.colorTW = await fillTermWrapper(opts.colorTW, app.vocabApi);
-    if (opts.shapeTW) opts.shapeTW = await fillTermWrapper(opts.shapeTW, app.vocabApi);
-    if (opts.scaleDotTW) opts.scaleDotTW = await fillTermWrapper(opts.scaleDotTW, app.vocabApi);
-  } catch (e) {
-    if (e.stack) console.log(e.stack);
-    throw new Error(`${e} [summary getPlotConfig()]`);
-  }
-  const config = {
-    chartType: "summary",
-    childType: "barchart",
-    term: opts.term,
-    groups: [],
-    controlLabels: Object.assign({}, defaultUiLabels, app.vocabApi.termdbConfig.uiLabels || {}),
-    //Allow hiding the plot filter when appropriate (e.g. single cell summary plots)
-    hidePlotFilter: opts.hidePlotFilter || false,
-    settings: {
-      controls: {
-        isOpen: false
-      },
-      common: {
-        use_logscale: false,
-        // flag for y-axis scale type, 0=linear, 1=log
-        use_percentage: false
-        // Move to barchart settings
-        // barheight: 300, // maximum bar length
-        // barwidth: 20, // bar thickness
-        // barspace: 2 // space between two bars
-      },
-      barchart: getDefaultBarSettings(app),
-      violin: getDefaultViolinSettings(app),
-      boxplot: getDefaultBoxplotSettings(app),
-      sampleScatter: getDefaultScatterSettings(opts)
-    },
-    mayAdjustConfig(config2, edits = {}) {
-      return mayAdjustConfig(config2, opts, edits);
-    }
-  };
-  if (config.term.term.type == "geneVariant") config.settings.barchart.colorBars = true;
-  copyMerge(config, opts);
-  Object.assign(config.controlLabels, app.vocabApi.termdbConfig.uiLabels || {});
-  return config;
-}
-function isScatterToggleVisible(appState, term, term2) {
-  const isSupportedChart = getCurrentCohortChartTypes(appState).includes("dynamicScatter");
-  return isSupportedChart && isNumericTw(term) && isNumericTw(term2);
-}
-var discreteByContinuousPlots = /* @__PURE__ */ new Set(["violin", "boxplot"]);
-function mayAdjustConfig(config, opts, edits = {}) {
-  if (edits.childType) {
-    if (config.childType != edits.childType) throw `action.config.childType was not applied in mass store.plot_edit()`;
-    return;
-  }
-  if (config.term?.q?.mode == "continuous" && config.term2?.q?.mode == "continuous") {
-    config.childType = "sampleScatter";
-  } else if (config.term?.term?.type == "termCollection" && config.term?.type !== "TermCollectionTWFraction") {
-    if (config.term.term.memberType == "categorical") {
-      config.childType = "barchart";
-    } else if (config.term.term.memberType == "numeric") {
-      if (config.childType) {
-        if (config.childType == "barchart") {
-          config.childType = "violin";
-        } else {
-        }
-      } else {
-        config.childType = "violin";
-      }
-    } else {
-      throw new Error("config.term.term.memberType not categorical or numeric");
-    }
-  } else if (config.term?.q?.mode == "continuous" || config.term2?.q?.mode == "continuous") {
-    if (!discreteByContinuousPlots.has(config.childType)) {
-      if (opts.childType && !discreteByContinuousPlots.has(opts.childType)) {
-        console.warn(
-          `ignoring summary opts.childType='${opts.childType}' since it does not support plotting discrete by continuous tw's`
-        );
-        config.childType = "violin";
-      } else {
-        config.childType = opts.childType || "violin";
-      }
-    }
-  } else {
-    config.childType = "barchart";
-  }
-}
-
-export {
-  summaryInit,
-  componentInit,
-  getPlotConfig,
-  isScatterToggleVisible,
-  mayAdjustConfig
-};
-//# sourceMappingURL=chunk-J5XV35LN.js.map

package/dist/chunk-JMWCL3QQ.js

@@ -1,56 +0,0 @@
-import {
-  sayerror
-} from "./chunk-4ASBDE27.js";
-import {
-  TermTypeGroups
-} from "./chunk-WJLRU5OF.js";
-
-// termdb/handlers/singleCellCellType.ts
-var SearchHandler = class {
-  async init(opts) {
-    this.validateOpts(opts);
-    this.callback = opts.callback;
-    this.app = opts.app;
-    const holder = opts.holder.append("div").style("padding", "10px 0px");
-    const scctTerms = opts.app.vocabApi.termdbConfig?.termType2terms?.[TermTypeGroups.SINGLECELL_CELLTYPE];
-    if (!scctTerms?.length) {
-      sayerror(
-        holder,
-        `termType2terms[${TermTypeGroups.SINGLECELL_CELLTYPE}]:[] is required in termdbConfig for singleCellCellType handler`
-      );
-      return;
-    }
-    const usecaseConfig = opts.usecase?.specialCase?.config;
-    const plots = usecaseConfig?.sample?.plots;
-    const isMeta = usecaseConfig?.sample?.isMetaResult;
-    const filtered = plots ? scctTerms.filter((t) => plots.includes(t.plot)) : usecaseConfig?.name ? scctTerms.filter((t) => t.plot === usecaseConfig.name) : scctTerms;
-    const getLabel = (t) => isMeta || plots?.length == 1 ? t.name : `${t.name} (${t.plot})`;
-    const filteredTerms = new Set(
-      plots || !usecaseConfig?.name ? filtered.map((t) => ({ ...t, label: getLabel(t) })) : filtered
-    );
-    for (const t of Array.from(filteredTerms)) {
-      holder.append("div").classed("termdiv", true).style("padding", "0px 5px").append("div").classed("termlabel sja_filter_tag_btn sja_tree_click_term ts_pill", true).style("display", "inline-block").style("padding", "5px 8px").style("margin", "1px 0px").style("border-radius", "6px").text(t.label || t.name).on("click", () => {
-        const term = this.makeTerm(t, usecaseConfig);
-        this.callback(term);
-      });
-    }
-  }
-  makeTerm(_term, usecaseConfig) {
-    const term = { ..._term };
-    if (!term.sample && usecaseConfig?.sample) term.sample = usecaseConfig.sample;
-    return term;
-  }
-  validateOpts(opts) {
-    if (opts.callback == null) throw new Error("callback is required");
-    if (opts.app == null) throw new Error("app is required");
-    if (opts.holder == null) throw new Error("holder is required");
-    if (opts.usecase == null) throw new Error("usecase is required");
-    if (!opts.app.vocabApi.termdbConfig?.termType2terms)
-      throw new Error("termType2terms is required in termdbConfig for singleCellCellType handler");
-  }
-};
-
-export {
-  SearchHandler
-};
-//# sourceMappingURL=chunk-JMWCL3QQ.js.map

package/dist/chunk-K3Q3KTBT.js

@@ -1,102 +0,0 @@
-import {
-  addGeneSearchbox,
-  first_genetrack_tolist,
-  getDNAMethUnit,
-  sayerror
-} from "./chunk-4ASBDE27.js";
-import {
-  Menu
-} from "./chunk-CNFTQSNE.js";
-import {
-  DNA_METHYLATION
-} from "./chunk-WJLRU5OF.js";
-
-// termdb/handlers/dnaMethylation.ts
-var SearchHandler = class {
-  init(opts) {
-    this.opts = opts;
-    this.callback = opts.callback;
-    this.app = opts.app;
-    const holder = opts.holder.append("div").style("margin", "10px 0px");
-    this.dom = {};
-    this.dom.errDiv = holder.append("div").style("margin", "5px 0px").style("display", "none");
-    this.dom.geneSearchDiv = holder.append("div");
-    this.dom.blockDiv = holder.append("div").style("display", "none").style("margin", "15px 4px");
-    const geneSearch = addGeneSearchbox({
-      tip: new Menu({ padding: "0px" }),
-      genome: opts.genomeObj,
-      row: this.dom.geneSearchDiv,
-      callback: async () => {
-        try {
-          this.dom.errDiv.style("display", "none");
-          await this.handleGeneSearch(geneSearch);
-        } catch (e) {
-          this.dom.errDiv.style("display", "block");
-          sayerror(this.dom.errDiv, "Error: " + (e.message || e));
-          if (e.stack) console.log(e.stack);
-        }
-      }
-    });
-  }
-  async handleGeneSearch(geneSearch) {
-    if (geneSearch.geneSymbol) {
-      const { chr, start, stop } = geneSearch;
-      if (!chr || !Number.isInteger(start) || !Number.isInteger(stop))
-        throw new Error("unable to retrieve gene coordinate");
-      this.dom.blockDiv.selectAll("*").remove();
-      this.dom.blockDiv.style("display", "block");
-      this.dom.blockDiv.append("div").style("opacity", 0.6).text("Navigate genome browser to desired region");
-      const arg = {
-        holder: this.dom.blockDiv,
-        genome: this.opts.genomeObj,
-        // genome obj
-        chr,
-        start,
-        stop,
-        tklst: [],
-        nobox: true,
-        width: 500,
-        hidegenelegend: true,
-        debugmode: this.opts.debug
-      };
-      first_genetrack_tolist(this.opts.genomeObj, arg.tklst);
-      const _ = await import("./block-53QIZEH3.js");
-      this.blockInstance = new _.Block(arg);
-      this.dom.submitBtn = this.dom.blockDiv.append("div").attr("data-testid", "sjpp-dnaMethylation-submitDiv").style("margin", "10px 0px").append("button").style("border", "none").style("border-radius", "20px").style("padding", "10px 15px").text("Submit Region").on("click", async () => {
-        const { chr: chr2, start: start2, stop: stop2 } = this.blockInstance.rglst[0];
-        const term = this.makeTerm({ chr: chr2, start: start2, stop: stop2 });
-        await this.callback(term);
-      });
-    } else if (geneSearch.chr && Number.isInteger(geneSearch.start) && Number.isInteger(geneSearch.stop)) {
-      const { chr } = geneSearch;
-      let { start, stop } = geneSearch;
-      if (geneSearch.actualposition?.len <= 1) {
-        start = geneSearch.actualposition.position;
-        stop = start + 1;
-      }
-      const term = this.makeTerm({ chr, start, stop });
-      await this.callback(term);
-    } else {
-      throw new Error("invalid gene search input");
-    }
-  }
-  makeTerm(opts) {
-    const { chr, start, stop } = opts;
-    if (!chr || !Number.isInteger(start) || !Number.isInteger(stop)) throw new Error("invalid coordinate");
-    const unit = getDNAMethUnit("region", this.app.vocabApi);
-    const term = {
-      chr,
-      start,
-      stop,
-      type: DNA_METHYLATION,
-      unit,
-      genomicFeatureType: "region"
-    };
-    return term;
-  }
-};
-
-export {
-  SearchHandler
-};
-//# sourceMappingURL=chunk-K3Q3KTBT.js.map